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- PDB-6jhi: Crystal structure of mutant D470A of Pullulanase from Paenibacill... -

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Basic information

Entry
Database: PDB / ID: 6jhi
TitleCrystal structure of mutant D470A of Pullulanase from Paenibacillus barengoltzii complexed with maltotetraose
ComponentsPulullanase
KeywordsHYDROLASE / GH13 / Pullulanase / maltotetraose
Function / homology
Function and homology information


pullulanase / pullulanase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Pullulanase, all-beta domain / Pullulanase, type I / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycosidases ...: / Pullulanase, all-beta domain / Pullulanase, type I / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Pulullanase
Similarity search - Component
Biological speciesPaenibacillus barengoltzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.319 Å
AuthorsWu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q.
CitationJournal: To Be Published
Title: Crystal structure of mutant D470A of Pullulanase from Paenibacillus barengoltzii complexed with maltotetraose
Authors: Wu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q.
History
DepositionFeb 18, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 6, 2019ID: 5WWA
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pulullanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3188
Polymers75,1401
Non-polymers1,1787
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-13 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.757, 98.517, 141.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Pulullanase


Mass: 75139.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-8 (MLSVQKEF) and 638-658(GASGEAAAAAPAAAGGPPAGG) had low-level electron density and were not included in the model.
Source: (gene. exp.) Paenibacillus barengoltzii (bacteria) / Strain: CAU940 / Plasmid: pET-28a(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0C5GWS2, pullulanase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08M calcium chloride, 0.1M MES, 22% PEG 3350, 0.7% beta-OG, pH 6.5
Temp details: 291-295

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 90-100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.319→50 Å / Num. obs: 30977 / % possible obs: 98.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.742
Reflection shellResolution: 2.319→2.36 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 7.778 / Num. unique obs: 1622 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX(1.13_2998: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E8Y

2e8y


Resolution: 2.319→38.068 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.07
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2103 1539 4.97 %
Rwork0.1532 --
obs0.156 30973 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.319→38.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5119 0 73 382 5574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085361
X-RAY DIFFRACTIONf_angle_d0.9297293
X-RAY DIFFRACTIONf_dihedral_angle_d5.5784371
X-RAY DIFFRACTIONf_chiral_restr0.056794
X-RAY DIFFRACTIONf_plane_restr0.006949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3192-2.3940.20831250.14882553X-RAY DIFFRACTION95
2.394-2.47950.24581260.15232664X-RAY DIFFRACTION99
2.4795-2.57880.24261670.16022659X-RAY DIFFRACTION99
2.5788-2.69610.25691450.1652678X-RAY DIFFRACTION100
2.6961-2.83820.21521350.17642674X-RAY DIFFRACTION98
2.8382-3.0160.27071320.182681X-RAY DIFFRACTION99
3.016-3.24870.22391430.1812689X-RAY DIFFRACTION100
3.2487-3.57550.24771450.16262704X-RAY DIFFRACTION99
3.5755-4.09230.18761310.13722683X-RAY DIFFRACTION98
4.0923-5.15390.1651450.12082707X-RAY DIFFRACTION97
5.1539-38.07290.17061450.15152742X-RAY DIFFRACTION94

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